iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species

Abstract

Gene regulatory circuits are often commonly shared between two closely related organisms. Our web tool iCR (identify Conserved target of a Regulon) makes use of this fact and identify conserved targets of a regulatory protein. iCR is a special refined extension of our previous tool PredictRegulon- that predicts genome wide, the potential binding sites and target operons of a regulatory protein in a single user selected genome. Like PredictRegulon, the iCR accepts known binding sites of a regulatory protein as ungapped multiple sequence alignment and provides the potential binding sites. However important differences are that the user can select more than one genome at a time and the output reports the genes that are common in two or more species. In order to achieve this, iCR makes use of Cluster of Orthologous Group (COG) indices for the genes. This tool analyses the upstream region of all user-selected prokaryote genome and gives the output based on conservation target orthologs. iCR also reports the Functional class codes based on COG classification for the encoded proteins of downstream genes which helps user understand the nature of the co-regulated genes at the result page itself. iCR is freely accessible at http://www.cdfd.org.in/icr/.

Figure 1

Architecture of iCR. iCR is a CGI application which collects input from user using html forms (A). B represents a Perl script that gathers the input from A launches the Search Engine (C) which looks up genome sequences and their annotations (D), and returns the potential targets as an output which is further classified based on COG/Class or Genome. The classified output is returned as HTML output (F).